plugin

Quantification of HER2 immunohistochemistry.

ImmunoMembrane is an ImageJ plugin for assessing HER2 immunohistochemistry, described in [bib]2472[/bib]. It is important to read the URL documentation and original paper to understand how to use the plugin appropriately.

There is web service available. Users can upload image data to process them and get cell membrane to be segmented: Web ImmunoMembrane

Note also that the pixel size is not read automatically from the image, but rather the source image scale should be entered into the dialog box - and the image rescaled accordingly prior to analysis. This scale value is the inverse of the value normally found for pixel width and pixel height under Image -> Properties... (i.e. pixel width & height are given in microns per pixel; the dialog box asks for pixels per micron).

For each ROI, provides the ratio of pixels over a given threshold over the total number of pixels in the ROI.

This method allows to compute a threshold that preserves the moments of an image. In ImageJ/Fiji, you can access it in Image->Ajust->Threshold and choose Moments in the list. In Aphelion, the tool is in Segmentation->Threshold->AphImgMomentThreshold The original paper is 2449

Analyzing Ca2+ sparks

ImageJ plugin to detect and measure Ca2+ sparks in linescan images, described in Picht et. al. (2007). The algorithm is based on that described by Cheng et al. (1999). Care should be taken to ensure that detections belong to 'true' events, as without any additional background subtraction steps the algorithm is not appropriate for images in which the baseline fluorescence varies substantially.

This tool allows for extraction of image series from Olympus Slide Scanners. These VSI files usually contain several images that are too big to load into memory (>50k x 50k pixels). It was written and tested on Fiji and is available from a Fiji Update Site: http://fiji.sc/List_of_update_sites